[CIG-SHORT] Trouble Installing Stable Pylith 1.5 -- petscmesh.hh not found

Wed Oct 20 15:53:18 PDT 2010

Hi Matt and Brad

First of all, thanks for the rapid replys.  The short story is that I
followed your suggestions and I still have the same question.  More complete
answers to your questions/suggestions are below.

Matt:
I built PETSc in the following manner.
1) I used "hg pull" then "hg update" in my petsc-dev folder
2) I cd'ed into my config/BuildSystem folder and did "hg pull" and "hg
update"
3) I configured PETSc using the following script:

    ARCH_FLAGS="--PETSC_ARCH=linux_${TOOLS_FORMAT}_opt --with-debugging=0"
    LANG_FLAGS="--with-clanguage=cxx"
    BUILD_FLAGS="--with-mpi-compilers=0 --with-gnu-compilers=1
--with-shared-libraries=1 --with-dynamic-loading=1 --with-64-bit-points=1
--with-large-file-io=1 --cc=gcc --cxx=g++ --fc=gfortran"
    MPI_FLAGS="--with-mpi-dir=${TOOLS_DIR}/mpich-1.2.1/gcc-4.1.1_64
--with-mpi-shared=0"
    OPTIONS="--with-lgrind=0 --with-c2html=0 "
    PART_FLAGS="--with-chaco=1 --download-chaco=1 --with-parmetis=1
--with-parmetis-dir=~/tools/ParMetis-3.1.1/${TOOLS_FORMAT}
--with-f-blas-lapack=1 --download-f-blas-lapack=1"
    SIEVE_FLAGS="--with-sieve=1 --download-sieve=1 --with-boost=1
--download-boost=1"
    config/configure.py ${ARCH_FLAGS} ${LANG_FLAGS} ${BUILD_FLAGS}
${MPI_FLAGS} ${OPTIONS} ${PART_FLAGS} ${SIEVE_FLAGS} ${EXTRA_FLAGS}

4) Following the advice of Barry Smith, I cd'ed into
src/dm/impls/da/ftn-custom and ran "make" in this folder
5) I ran "make fortranstubs" in my petsc-dev folder
6) I ran "make" and then "make test" in my petsc-dev folder

Make test is successful.  As you can see, I do have my clanguage set to cxx.

Brad:
I've reconfigured and rebuilt PETSc and Pylith, and I have run into the same
error.  My configuration script for Pylith is:

./configure > configure.log --enable-swig --enable-testing --enable-cubit
--prefix=${CIG_DIR}  CPPFLAGS="-I${PROJ4_INCDIR} -I${CPPUNIT_INCDIR}
-I${CIG_INCDIR} -I${PYTHIA_INCDIR} -I${NETCDF_INCDIR}"
LDFLAGS="-L${PROJ4_LIBDIR} -L${CPPUNIT_LIBDIR} -L${CIG_LIBDIR}
-L${NETCDF_LIBDIR}"  LIBS=""  CC=gcc CXX=g++ FC=gfortran F77=gfortran

Is there anything that I'm missing from this configuration that may be
causing my problem?

Thanks again,
Jeff Thompson
Seismolab
California Institute of Technology

On Wed, Oct 20, 2010 at 2:42 PM, Brad Aagaard <baagaard at usgs.gov> wrote:

> Jeff,
>
> Try reconfiguring and rebuilding Petsc and then pylith. There have been
> recent changes to the petsc build system that required changes to the pylith
> configure to keep them in sync.
>
> Brad
>
>
>
> On Oct 20, 2010, at 2:12 PM, Jeffrey Thompson <jeffremt at gmail.com> wrote:
>
> > Hello CIG-Short,
> >
> > I'm trying to make and install the stable version of Pylith, and I ran
> into the error below after issuing the "make" command.  It seems to me that
> the main error is that Pylith cannot find the petscmesh.hh file.  I updated
> PETSc and spatialdata before Pylith, so I should have the most recent
> versions of these programs.  I also tried installing the version Pylith from
> the trunk directory, and the same error occured.  I've attached my
> config.log file from the 'stable' pylith install.
> >
> > Thanks in advance,
> > Jeff Thompson
> > Seismolab
> > California Institute of Technology
> >
> > make[3]: Entering directory `/home/jeffremt/tools/cig/v1.5-stable/libsrc'
> > if /bin/sh ../libtool --mode=compile --tag=CXX g++ -DHAVE_CONFIG_H -I.
> -I. -I.. -I../include
>  -I/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.11-py2.5.egg
> -I/usr/include/python2.5  -DENABLE_CUBIT
> -I/home/jeffremt/tools/proj-4.7.0/gcc-4.1.1_64/include
> -I/home/jeffremt/tools/cppunit-1.12.1/gcc-4.1.1_64/include
> -I/home/jeffremt/tools/cig/gcc-4.1.1_64/include
> -I/home/jeffremt/tools/cig/gcc-4.1.1_64/include/pythia-0.8.1.10
> -I/home/jeffremt/tools/netcdf-4.0.1/gcc-4.1.1_64/include  -g -O2 -MT
> BoundaryCondition.lo -MD -MP -MF ".deps/BoundaryCondition.Tpo" -c -o
> BoundaryCondition.lo `test -f 'bc/BoundaryCondition.cc' || echo
> './'`bc/BoundaryCondition.cc; \
> > then mv -f ".deps/BoundaryCondition.Tpo" ".deps/BoundaryCondition.Plo";
> else rm -f ".deps/BoundaryCondition.Tpo"; exit 1; fi
> > mkdir .libs
> >  g++ -DHAVE_CONFIG_H -I. -I. -I.. -I../include
> -I/home/jeffremt/tools/cig/gcc-4.1.1_64/lib/python2.5/site-packages/pythia-0.8.1.11-py2.5.egg
> -I/usr/include/python2.5 -DENABLE_CUBIT
> -I/home/jeffremt/tools/proj-4.7.0/gcc-4.1.1_64/include
> -I/home/jeffremt/tools/cppunit-1.12.1/gcc-4.1.1_64/include
> -I/home/jeffremt/tools/cig/gcc-4.1.1_64/include
> -I/home/jeffremt/tools/cig/gcc-4.1.1_64/include/pythia-0.8.1.10
> -I/home/jeffremt/tools/netcdf-4.0.1/gcc-4.1.1_64/include -g -O2 -MT
> BoundaryCondition.lo -MD -MP -MF .deps/BoundaryCondition.Tpo -c
> bc/BoundaryCondition.cc  -fPIC -DPIC -o .libs/BoundaryCondition.o
> > In file included from bc/BoundaryCondition.cc:23:
> > ../include/pylith/topology/Mesh.hh:33:43: petscmesh.hh: No such file or
> directory
> > In file included from bc/BoundaryCondition.cc:23:
> > ../include/pylith/topology/Mesh.hh:59: error: `ALE' has not been declared
> > ../include/pylith/topology/Mesh.hh:59: error: ISO C++ forbids declaration
> of `IMesh' with no type
> > ../include/pylith/topology/Mesh.hh:59: error: expected `;' before '<'
> token
> > ../include/pylith/topology/Mesh.hh:60: error: `SieveMesh' has not been
> declared
> > ../include/pylith/topology/Mesh.hh:60: error: ISO C++ forbids declaration
> of `real_section_type' with no type
> > ../include/pylith/topology/Mesh.hh:60: error: expected `;' before
> "RealSection"
> > ../include/pylith/topology/Mesh.hh:61: error: `SieveMesh' has not been
> declared
> > ../include/pylith/topology/Mesh.hh:61: error: ISO C++ forbids declaration
> of `int_section_type' with no type
> > ../include/pylith/topology/Mesh.hh:61: error: expected `;' before
> "IntSection"
> > ../include/pylith/topology/Mesh.hh:62: error: `ALE' has not been declared
> > ../include/pylith/topology/Mesh.hh:62: error: ISO C++ forbids declaration
> of `IMesh' with no type
> > ../include/pylith/topology/Mesh.hh:62: error: expected `;' before '<'
> token
> > ../include/pylith/topology/Mesh.hh:63: error: `ALE' has not been declared
> > ../include/pylith/topology/Mesh.hh:63: error: ISO C++ forbids declaration
> of `RestrictVisitor' with no type
> > ../include/pylith/topology/Mesh.hh:63: error: expected `;' before '<'
> token
> > ../include/pylith/topology/Mesh.hh:64: error: `ALE' has not been declared
> > ../include/pylith/topology/Mesh.hh:64: error: ISO C++ forbids declaration
> of `UpdateAddVisitor' with no type
> > ../include/pylith/topology/Mesh.hh:64: error: expected `;' before '<'
> token
> > ../include/pylith/topology/Mesh.hh:65: error: `ALE' has not been declared
> > ../include/pylith/topology/Mesh.hh:65: error: ISO C++ forbids declaration
> of `UpdateAllVisitor' with no type
> > ../include/pylith/topology/Mesh.hh:65: error: expected `;' before '<'
> token
> > ../include/pylith/topology/Mesh.hh:66: error: `ALE' has not been declared
> > ../include/pylith/topology/Mesh.hh:66: error: ISO C++ forbids declaration
> of `IndicesVisitor' with no type
> > ../include/pylith/topology/Mesh.hh:66: error: expected `;' before '<'
> token
> > ../include/pylith/topology/Mesh.hh:82: error: expected `,' or `...'
> before '&' token
> > ../include/pylith/topology/Mesh.hh:82: error: ISO C++ forbids declaration
> of `MPI_Comm' with no type
> > ../include/pylith/topology/Mesh.hh:100: error: `ALE' has not been
> declared
> > ../include/pylith/topology/Mesh.hh:100: error: ISO C++ forbids
> declaration of `Obj' with no type
> > ../include/pylith/topology/Mesh.hh:100: error: expected `;' before '<'
> token
> > ../include/pylith/topology/Mesh.hh:106: error: `ALE' has not been
> declared
> > ../include/pylith/topology/Mesh.hh:106: error: ISO C++ forbids
> declaration of `Obj' with no type
> > ../include/pylith/topology/Mesh.hh:106: error: expected `;' before '<'
> token
> > ../include/pylith/topology/Mesh.hh:160: error: expected `,' or `...'
> before "value"
> > ../include/pylith/topology/Mesh.hh:160: error: ISO C++ forbids
> declaration of `MPI_Comm' with no type
> > ../include/pylith/topology/Mesh.hh:166: error: `MPI_Comm' does not name a
> type
> > ../include/pylith/topology/Mesh.hh:195: error: `ALE' has not been
> declared
> > ../include/pylith/topology/Mesh.hh:195: error: ISO C++ forbids
> declaration of `Obj' with no type
> > ../include/pylith/topology/Mesh.hh:195: error: expected `;' before '<'
> token
> > ../include/pylith/topology/Mesh.hh:197: error: `MPI_Comm' does not name a
> type
> > In file included from ../include/pylith/topology/Mesh.hh:208,
> >                  from bc/BoundaryCondition.cc:23:
> > ../include/pylith/topology/Mesh.icc:25: error: `ALE' has not been
> declared
> > ../include/pylith/topology/Mesh.icc:25: error: expected initializer
> before '<' token
> > ../include/pylith/topology/Mesh.icc:32: error: `ALE' has not been
> declared
> > ../include/pylith/topology/Mesh.icc:32: error: expected initializer
> before '<' token
> > ../include/pylith/topology/Mesh.icc: In member function `void
> pylith::topology::Mesh::debug(bool)':
> > ../include/pylith/topology/Mesh.icc:49: error: `_mesh' was not declared
> in this scope
> > ../include/pylith/topology/Mesh.icc: In member function `int
> pylith::topology::Mesh::dimension() const':
> > ../include/pylith/topology/Mesh.icc:64: error: `_mesh' was not declared
> in this scope
> > ../include/pylith/topology/Mesh.icc: In member function `int
> pylith::topology::Mesh::coneSize() const':
> > ../include/pylith/topology/Mesh.icc:71: error: `_mesh' was not declared
> in this scope
> > ../include/pylith/topology/Mesh.icc: In member function `int
> pylith::topology::Mesh::numVertices() const':
> > ../include/pylith/topology/Mesh.icc:78: error: `_mesh' was not declared
> in this scope
> > ../include/pylith/topology/Mesh.icc: In member function `int
> pylith::topology::Mesh::numCells() const':
> > ../include/pylith/topology/Mesh.icc:85: error: `_mesh' was not declared
> in this scope
> > ../include/pylith/topology/Mesh.icc: At global scope:
> > ../include/pylith/topology/Mesh.icc:91: error: expected `,' or `...'
> before "value"
> > ../include/pylith/topology/Mesh.icc:91: error: ISO C++ forbids
> declaration of `MPI_Comm' with no type
> > ../include/pylith/topology/Mesh.icc: In member function `void
> pylith::topology::Mesh::comm(int)':
> > ../include/pylith/topology/Mesh.icc:92: error: `_comm' was not declared
> in this scope
> > ../include/pylith/topology/Mesh.icc:92: error: `value' was not declared
> in this scope
> > ../include/pylith/topology/Mesh.icc: At global scope:
> > ../include/pylith/topology/Mesh.icc:97: error: `MPI_Comm' does not name a
> type
> > ../include/pylith/topology/Mesh.icc: In member function `void
> pylith::topology::Mesh::view(const char*) const':
> > ../include/pylith/topology/Mesh.icc:106: error: `_mesh' was not declared
> in this scope
> > bc/BoundaryCondition.cc: In member function `virtual void
> pylith::bc::BoundaryCondition::verifyConfiguration(const
> pylith::topology::Mesh&) const':
> > bc/BoundaryCondition.cc:53: error: `ALE' has not been declared
> > bc/BoundaryCondition.cc:53: error: expected initializer before '<' token
> > bc/BoundaryCondition.cc:54: error: `sieveMesh' was not declared in this
> scope
> > bc/BoundaryCondition.cc:57: error: aggregate `std::ostringstream msg' has
> incomplete type and cannot be defined
> > make[3]: *** [BoundaryCondition.lo] Error 1
> > make[3]: Leaving directory `/home/jeffremt/tools/cig/v1.5-stable/libsrc'
> > make[2]: *** [all-recursive] Error 1
> > make[2]: Leaving directory `/home/jeffremt/tools/cig/v1.5-stable/libsrc'
> > make[1]: *** [all-recursive] Error 1
> > make[1]: Leaving directory `/home/jeffremt/tools/cig/v1.5-stable'
> > make: *** [all] Error 2
> >
> > <config.log>
> > _______________________________________________
> > CIG-SHORT mailing list
> > CIG-SHORT at geodynamics.org
> > http://geodynamics.org/cgi-bin/mailman/listinfo/cig-short
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: http://geodynamics.org/pipermail/cig-short/attachments/20101020/d23033ba/attachment-0001.htm 